Il giorno 26 mar 2020, alle ore 2:44 PM, freesurfer-request@nmr.mgh.harvard.edu ha scritto:

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Today's Topics:

  1. Re: Misalignment of boundaries and T1 (Freesurfer/SamSrf)
     (Mason Wells)
  2. Re: VM_setup (fsbuild)
  3. Re: mri_deface download link not found (Hoopes, Andrew)
  4. Registration file types confusion (Xiaojiang Yang)
  5. Freeview CLI feature request (VINCENT KOPPELMANS)
  6. Re: Freeview CLI feature request (Ruopeng Wang)
  7. Re: Freeview CLI feature request (VINCENT KOPPELMANS)
  8. Re: training set (javier quilis)
  9. Re: Misalignment of boundaries and T1 (Freesurfer/SamSrf)
     (Mason Wells)
10. Re: Hippocampal Volume Extraction (Devika K)
11. Re: training set (Bruce Fischl)
12. Re: Misalignment of boundaries and T1 (Freesurfer/SamSrf)
     (Bruce Fischl)

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Message: 1
Date: Wed, 25 Mar 2020 18:38:34 +0000
From: Mason Wells <WellsMT1@cardiff.ac.uk>
Subject: Re: [Freesurfer] Misalignment of boundaries and T1
(Freesurfer/SamSrf)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5BD22FFC-C541-42CB-964B-AA3B2186428F@cardiff.ac.uk>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution

HI Bruce,

Ok, great. I just thought some sections of white matter had not been traced in their entirety (see red crosshair in attached image). If you think this all looks reasonable, please can you advise on the misaligned as outlined in the original post?

Best wishes,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau?r Golwg
& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: WellsMT1@caerdydd.ac.uk
Ff?n: 02920 879628

?On 25/03/2020, 17:29, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

   Hi Mason

   I can't tell from those images except that it looks reasonable
   cheers
   Bruce
   On Wed, 25
   Mar 2020, Mason Wells wrote:

      External Email - Use Caution

Hi again Bruce,

I have now installed the relevant libpng packages and have freeview open. The segmentation doesn?t look brilliant in some areas. What do you think?

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau?r Golwg
& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: WellsMT1@caerdydd.ac.uk
Ff?n: 02920 879628

On 25/03/2020, 16:28, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@cardiff.ac.uk> wrote:

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  Hi Bruce,

  I get the following error message when I try to load freeview

  Setting up environment for FreeSurfer/FS-FAST (and FSL)
  FREESURFER_HOME   /usr/local/freesurfer
  FSFAST_HOME       /usr/local/freesurfer/fsfast
  FSF_OUTPUT_FORMAT nii.gz
  SUBJECTS_DIR      /usr/local/freesurfer/subjects
  MNI_DIR           /usr/local/freesurfer/mni
  FSL_DIR           /usr/local/fsl
  masontwells@masontwells-VIG800S:~$ freeview
  freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory

  Mason T Wells, MSc
  PhD student
  School of Optometry and Vision Sciences
  & Cardiff University Brain Research
  Imaging Centre (CUBRIC), School of Psychology
  Cardiff University
  Cardiff
  CF24 4HQ
  UK

  Email: WellsMT1@cardiff.ac.uk
  Tel: 02920 879628
  Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
  Mason T Wells, MSc
  Myfyriwr PhD
  Yr Ysgol Optometreg a Gwyddorau?r Golwg
  & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
  Prifysgol Caerdydd
  Heol Maindy
  Caerdydd
  CF24 4HQ
  DU

  E-bost: WellsMT1@caerdydd.ac.uk
  Ff?n: 02920 879628

  On 25/03/2020, 16:19, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

      something like

      freeview -v $SUBJECTS_DIR/<subject name>/mri/norm.mgz \
        -f $SUBJECTS_DIR/<subject name>/surf/?h.white

      cheers
      Bruce

      On Wed, 25 Mar 2020, Mason Wells wrote:

      External Email - Use Caution

Hi Bruce,

Thanks for getting back to me. Sorry, but I am not sure I follow what you mean here.
Could you please explain how I would check this?

Thanks again for your help.
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau?r Golwg
& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: WellsMT1@caerdydd.ac.uk
Ff?n: 02920 879628

On 25/03/2020, 16:11, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

  Hi Mason

  can you confirm that things look ok within FreeSurfer if you look at the
  surface over the volume in freeview?

  cheers
  Bruce
  On Wed, 25 Mar 2020, Mason Wells wrote:

       External Email - Use Caution

Hello Freesurfer developers,

I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all
command which finished without errors. However, the white/grey matter
boundaries are significantly misaligned with the subjects T1 (images
attached). Below are the steps I have taken to reach this point in the
analysis:

1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
2. Ran Feat

?         Distortion correction of the EPI

?         Motion correction

?         No smoothing

?         Highpass filter

?         No registration to whole brain

?         Register to T1_biascorr_brain

?         Register to standard space

3. Ran recon-all on T1_biascorr
4. Convert T1/T1_brain/orig(001) from mgz to nii
5. Check registration (using the SurfaceProjection command from the SamSrf
   package) which leads to the attached images named S1 and S1.

Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Platform: Linux 5.3.0-40-generic x86_64

Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon
Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

As you can see, the registration is significantly misaligned.

Can anyone offer any advice on this/suggest a way to rectify it?

Thanks in advance,

Mason

Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

Email: WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau?r Golwg

& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

E-bost: WellsMT1@caerdydd.ac.uk

Ff?n: 02920 879628

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Message: 2
Date: Wed, 25 Mar 2020 20:05:22 +0100
From: fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] VM_setup
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1585163122.5e7bab72c2100@trashmail.com>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution

Hello Pierpaolo,

Just sent it to your email.  You can email me back directly if you need something.

- R.On Mar 25, 2020, at 14:34, Pierpaolo Croce <pierpaolo12croce@gmail.com> wrote:        External Email - Use Caution        Dear List, I have followed the virtual machine setup for virtual box freesurfer installation... Starting ubuntu, ask me developers account informations. Which is the password?-- Ing. Pierpaolo Croce, PhD.Institute for Advanced Biomedical Technologies - ITABandDepartment of Neuroscience and ImagingUniversity of Chieti "G. D'Annunzio"Via dei Vestini, 3366013 Chieti, Italy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 3
Date: Wed, 25 Mar 2020 19:24:32 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_deface download link not found
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <A395AA58-1246-4D83-9478-B19277111303@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Ah thanks Tim, I misread. The links on that wiki page are fixed now. Sorry for the confusion.
Andrew

?On 3/25/20, 3:32 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Sch?fer" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ts+ml@rcmd.org> wrote:

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   I think the problem is not with running the version he downloaded, but the fact that he could not download it, because all download links on the website at https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface are dead.

   I downloaded mri_deface from that website about a month ago, back then the links were still okay. It seems something went wrong on the server in the meantime.

   Best,

   Tim

On March 24, 2020 at 6:39 PM "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu> wrote:

Hi Hailey,

Can you provide some more info about your issue, like what version you downloaded and a copy/paste of the command line you ran with the error message.

Thanks
Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "D'Silva, Hailey" <hailey.mulder@yale.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, March 24, 2020 at 7:24 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_deface download link not found

       External Email - Use Caution
Hello Freesurfer Experts!
I'm trying to anonymize a number of T1s by using mri_deface, but am getting a "Not Found" error when I try to download the tools for it.

Thanks for your help,
Hailey

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   _______________________________________________
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------------------------------

Message: 4
Date: Wed, 25 Mar 2020 16:00:53 -0500
From: Xiaojiang Yang <xjyangxj@gmail.com>
Subject: [Freesurfer] Registration file types confusion
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAPg=14aWe4zMno5fbWfZyNhz22bS1aMx0KYXwd36efLFJRRi2w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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Hi everyone,

I am confused by the two types of registration files: .lta and .dat.

.dat file is simpler and easier to understand. But for the .lta files,
there seems to be no detailed explanation regarding it. Can anyone point
out to me where can I find the detail explanation of the file? And, what's
the relationship between .lta and .dat file?

Also, .lta files seem to cause some compatibility issues. For example, if I
use the tkregister2 utility to make some changes to the registration file
of type .lta (generated by bbregister), like below

tkregister2 --mov $someSeries --reg
$SUBJECTS_DIR/$subjectid/mri/transforms/FLAIR.auto.lta --surf pial

and save it from the GUI, then many errors occur in the console window,
like below:
......
MatrixAsciiReadFrom: could not scanf parms
ERROR: TransformLTA2RegDat(): type = 2011264000, must be 1 or 0 or 14
Segmentation fault (core dumped)

Actually that is because the registration file has been saved in the format
of .dat, although the file extension is still .lta, and the tkregister2
program finally cracks when reading the newly saved .lta file.

Anyone can solve my confusion? Thank you!
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Message: 5
Date: Wed, 25 Mar 2020 22:28:00 +0000
From: VINCENT KOPPELMANS <vincent.koppelmans@utah.edu>
Subject: [Freesurfer] Freeview CLI feature request
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <FA7720A8-9593-4854-BD0E-4EEA17B7B339@contoso.com>
Content-Type: text/plain; charset="utf-8"

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Dear FreeSurfer team,

I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39

Would it be possible to add the following features as command line flags to FreeView?

1) Set opacity for a surface
It is currently only possible via CLI to set opacity for volumes, surface overlays, and labels, but not for the surface itself.

2) Set smoothing iterations for isosurfaces
This can only be done in the GUI, not yet via the CLI.

Thank you for your consideration.

- Vincent
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Message: 6
Date: Wed, 25 Mar 2020 18:41:02 -0400
From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freeview CLI feature request
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <6989E259-5D80-4BE4-8039-394262F86A78@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Sure. We?ll add those in.

Best,
Ruopeng

On Mar 25, 2020, at 6:28 PM, VINCENT KOPPELMANS <vincent.koppelmans@utah.edu> wrote:

       External Email - Use Caution

Dear FreeSurfer team,

I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39

Would it be possible to add the following features as command line flags to FreeView?

1) Set opacity for a surface
It is currently only possible via CLI to set opacity for volumes, surface overlays, and labels, but not for the surface itself.

2) Set smoothing iterations for isosurfaces
This can only be done in the GUI, not yet via the CLI.

Thank you for your consideration.

- Vincent
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Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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Message: 7
Date: Wed, 25 Mar 2020 22:43:44 +0000
From: VINCENT KOPPELMANS <vincent.koppelmans@utah.edu>
Subject: Re: [Freesurfer] Freeview CLI feature request
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <06F52328-176F-4D3C-BD29-EF8E70BD69E4@umail.utah.edu>
Content-Type: text/plain; charset="utf-8"

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Thank you for your quick and positive reply.

Best,
Vincent

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 25 March 2020 at 16:41
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freeview CLI feature request

Sure. We?ll add those in.

Best,
Ruopeng

On Mar 25, 2020, at 6:28 PM, VINCENT KOPPELMANS <vincent.koppelmans@utah.edu <mailto:vincent.koppelmans@utah.edu>> wrote:

       External Email - Use Caution

Dear FreeSurfer team,

I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39

Would it be possible to add the following features as command line flags to FreeView?

1) Set opacity for a surface
It is currently only possible via CLI to set opacity for volumes, surface overlays, and labels, but not for the surface itself.

2) Set smoothing iterations for isosurfaces
This can only be done in the GUI, not yet via the CLI.

Thank you for your consideration.

- Vincent
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 8
Date: Thu, 26 Mar 2020 11:15:47 +0000
From: javier quilis <j.quilis@hotmail.com>
Subject: Re: [Freesurfer] training set
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<HE1PR0602MB3385849CBF77626970C2C5EB90CF0@HE1PR0602MB3385.eurprd06.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

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Hi Bruce,

thanks for the answer. Is there any paper where this is explained? I want to detail this in my paper and I would like to refer to the source.

Thanks again,
Javier

________________________________
De: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> en nombre de Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Enviado: mi?rcoles, 25 de marzo de 2020 14:40
Para: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Asunto: Re: [Freesurfer] training set

Hi Javier

no, that's not correct, depending on which training set you mean. For the
Bayesian segmentation (aseg) we used 40 datasets distributed in age and
pathology (10 each for young, middle age, elderly and AD).

cheers
Bruce
On Wed, 25 Mar
2020, javier quilis wrote:

       External Email - Use Caution

Thanks for the answer.

I can not open the power point for some reason. Is there any paper where I
can check this? I think the dataset used by freesurfer is in the MNI Average
Brain (305 MRI) Stereotaxic Model and this dataset only use MRIs from young
people, is this correct?

Thanks again.
Bests,
Javier

____________________________________________________________________________
De: freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu> en nombre de Douglas N. Greve
<dgreve@mgh.harvard.edu>
Enviado: viernes, 20 de marzo de 2020 15:39
Para: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Asunto: Re: [Freesurfer] training set
Try the tutorial slides
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
It does not go into a lot of detail, but it will give you the relevant
lectures

On 3/17/2020 8:54 AM, javier quilis wrote:

             External Email - Use Caution

     Hello everyone,

I'm trying to do a study of a comparison between the automated methods
to analyze structural MRI from FSL and Freesurfer. I am interested in
the training set used by Freesurfer to do the brain segmentation and I
can not find a detailed description of it. Is there any source where
this set is described?

Thanks in advance.
Bests,
Javier Quilis

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Message: 9
Date: Thu, 26 Mar 2020 13:25:25 +0000
From: Mason Wells <WellsMT1@cardiff.ac.uk>
Subject: Re: [Freesurfer] Misalignment of boundaries and T1
(Freesurfer/SamSrf)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <9F66CFB7-6712-4267-BEA8-5577D1598C65@cardiff.ac.uk>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution

In the event that Bruce might not be able to help. I ask if anyone else on the list has experience with the problem described in this thread? Any help would be greatly appreciated.

Best wishes,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau?r Golwg
& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: WellsMT1@caerdydd.ac.uk
Ff?n: 02920 879628

?On 25/03/2020, 18:38, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@cardiff.ac.uk> wrote:

           External Email - Use Caution

   HI Bruce,

   Ok, great. I just thought some sections of white matter had not been traced in their entirety (see red crosshair in attached image). If you think this all looks reasonable, please can you advise on the misaligned as outlined in the original post?

   Best wishes,
   Mason

   Mason T Wells, MSc
   PhD student
   School of Optometry and Vision Sciences
   & Cardiff University Brain Research
   Imaging Centre (CUBRIC), School of Psychology
   Cardiff University
   Cardiff
   CF24 4HQ
   UK

   Email: WellsMT1@cardiff.ac.uk
   Tel: 02920 879628
   Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
   Mason T Wells, MSc
   Myfyriwr PhD
   Yr Ysgol Optometreg a Gwyddorau?r Golwg
   & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
   Prifysgol Caerdydd
   Heol Maindy
   Caerdydd
   CF24 4HQ
   DU

   E-bost: WellsMT1@caerdydd.ac.uk
   Ff?n: 02920 879628

   On 25/03/2020, 17:29, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

       Hi Mason

       I can't tell from those images except that it looks reasonable
       cheers
       Bruce
       On Wed, 25
       Mar 2020, Mason Wells wrote:

      External Email - Use Caution

Hi again Bruce,

I have now installed the relevant libpng packages and have freeview open. The segmentation doesn?t look brilliant in some areas. What do you think?

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau?r Golwg
& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: WellsMT1@caerdydd.ac.uk
Ff?n: 02920 879628

On 25/03/2020, 16:28, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@cardiff.ac.uk> wrote:

          External Email - Use Caution

  Hi Bruce,

  I get the following error message when I try to load freeview

  Setting up environment for FreeSurfer/FS-FAST (and FSL)
  FREESURFER_HOME   /usr/local/freesurfer
  FSFAST_HOME       /usr/local/freesurfer/fsfast
  FSF_OUTPUT_FORMAT nii.gz
  SUBJECTS_DIR      /usr/local/freesurfer/subjects
  MNI_DIR           /usr/local/freesurfer/mni
  FSL_DIR           /usr/local/fsl
  masontwells@masontwells-VIG800S:~$ freeview
  freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory

  Mason T Wells, MSc
  PhD student
  School of Optometry and Vision Sciences
  & Cardiff University Brain Research
  Imaging Centre (CUBRIC), School of Psychology
  Cardiff University
  Cardiff
  CF24 4HQ
  UK

  Email: WellsMT1@cardiff.ac.uk
  Tel: 02920 879628
  Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
  Mason T Wells, MSc
  Myfyriwr PhD
  Yr Ysgol Optometreg a Gwyddorau?r Golwg
  & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
  Prifysgol Caerdydd
  Heol Maindy
  Caerdydd
  CF24 4HQ
  DU

  E-bost: WellsMT1@caerdydd.ac.uk
  Ff?n: 02920 879628

  On 25/03/2020, 16:19, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

      something like

      freeview -v $SUBJECTS_DIR/<subject name>/mri/norm.mgz \
        -f $SUBJECTS_DIR/<subject name>/surf/?h.white

      cheers
      Bruce

      On Wed, 25 Mar 2020, Mason Wells wrote:

      External Email - Use Caution

Hi Bruce,

Thanks for getting back to me. Sorry, but I am not sure I follow what you mean here.
Could you please explain how I would check this?

Thanks again for your help.
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau?r Golwg
& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: WellsMT1@caerdydd.ac.uk
Ff?n: 02920 879628

On 25/03/2020, 16:11, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

  Hi Mason

  can you confirm that things look ok within FreeSurfer if you look at the
  surface over the volume in freeview?

  cheers
  Bruce
  On Wed, 25 Mar 2020, Mason Wells wrote:

       External Email - Use Caution

Hello Freesurfer developers,

I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all
command which finished without errors. However, the white/grey matter
boundaries are significantly misaligned with the subjects T1 (images
attached). Below are the steps I have taken to reach this point in the
analysis:

1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
2. Ran Feat

?         Distortion correction of the EPI

?         Motion correction

?         No smoothing

?         Highpass filter

?         No registration to whole brain

?         Register to T1_biascorr_brain

?         Register to standard space

3. Ran recon-all on T1_biascorr
4. Convert T1/T1_brain/orig(001) from mgz to nii
5. Check registration (using the SurfaceProjection command from the SamSrf
   package) which leads to the attached images named S1 and S1.

Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Platform: Linux 5.3.0-40-generic x86_64

Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon
Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

As you can see, the registration is significantly misaligned.

Can anyone offer any advice on this/suggest a way to rectify it?

Thanks in advance,

Mason

Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

Email: WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau?r Golwg

& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

E-bost: WellsMT1@caerdydd.ac.uk

Ff?n: 02920 879628

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7C4519acd1ab7442b9876108d7d0ebc5f4%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637207583376235974&sdata=WaOEstHSEO9vc8uZQ0jSf4I9rFYplWeXH5mFv5tDVrM%3D&reserved=0

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  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
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------------------------------

Message: 10
Date: Thu, 26 Mar 2020 19:02:11 +0530
From: Devika K <devikakuttala@gmail.com>
Subject: Re: [Freesurfer] Hippocampal Volume Extraction
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CA+m7eQEugcK9hM3M0_ouwC6MXoG=VnL4ShDL9PL9U-dT=kR1vA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution

Hi,

I want to extract hippocampal volume from longitudinal samples. I am less
aware of it. I ran recon-all-all with longitudinal pipeline for all those
samples.

How I need to process further (Commands that I need to follow).
Would you please help me out?

Thanks and Regards
Devika K
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------------------------------

Message: 11
Date: Thu, 26 Mar 2020 09:36:02 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] training set
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.21.2003260935250.13248@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"

Have you checked the original aseg paper? If not, then it will be in
Rahul's cortical parcellation one as it is the same data

cheers
Bruce

On Thu, 26 Mar 2020, javier quilis wrote:

????????External Email - Use Caution????????

Hi Bruce,?

thanks for the answer. Is there any paper where this is explained? I want to
detail this in my paper and I would like to refer to the source.?

Thanks again,?
Javier

____________________________________________________________________________
De: freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu> en nombre de Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
Enviado: mi?rcoles, 25 de marzo de 2020 14:40
Para: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Asunto: Re: [Freesurfer] training set ?
Hi Javier

no, that's not correct, depending on which training set you mean. For the
Bayesian segmentation (aseg) we used 40 datasets distributed in age and
pathology (10 each for young, middle age, elderly and AD).

cheers
Bruce
On Wed, 25 Mar
2020, javier quilis wrote:

????????External Email - Use Caution????????

Thanks for the answer.?

I can not open the power point for some reason. Is there any paper where I
can check this? I think the dataset used by freesurfer is in the MNI

Average

Brain (305 MRI) Stereotaxic Model and this dataset only use MRIs from

young

people, is this correct?

Thanks again.
Bests,?
Javier

___________________________________________________________________________

_

De: freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu> en nombre de Douglas N. Greve
<dgreve@mgh.harvard.edu>
Enviado: viernes, 20 de marzo de 2020 15:39
Para: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Asunto: Re: [Freesurfer] training set ?
Try the tutorial slides
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
It does not go into a lot of detail, but it will give you the relevant
lectures

On 3/17/2020 8:54 AM, javier quilis wrote:

?????? ????????External Email - Use Caution????????

?????? Hello everyone,?

I'm trying to do a study of a comparison between the automated methods
to analyze structural MRI from FSL and Freesurfer. I am interested in
the training set used by Freesurfer to do the brain segmentation and I
can not find a detailed description of it. Is there any source where
this set is described?

Thanks in advance.
Bests,?
Javier Quilis

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

------------------------------

Message: 12
Date: Thu, 26 Mar 2020 09:44:08 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Misalignment of boundaries and T1
(Freesurfer/SamSrf)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.21.2003260943340.13248@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Mason

not sure we can help if everything looks good in freeview. Doesn't that
make it a SamSrf issue? Or an interface between the two packages? Have you
checked with their support?

cheers
Bruce

On Thu, 26 Mar 2020, Mason Wells wrote:

      External Email - Use Caution

In the event that Bruce might not be able to help. I ask if anyone else on the list has experience with the problem described in this thread? Any help would be greatly appreciated.

Best wishes,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau?r Golwg
& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: WellsMT1@caerdydd.ac.uk
Ff?n: 02920 879628

?On 25/03/2020, 18:38, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@cardiff.ac.uk> wrote:

          External Email - Use Caution

  HI Bruce,

  Ok, great. I just thought some sections of white matter had not been traced in their entirety (see red crosshair in attached image). If you think this all looks reasonable, please can you advise on the misaligned as outlined in the original post?

  Best wishes,
  Mason

  Mason T Wells, MSc
  PhD student
  School of Optometry and Vision Sciences
  & Cardiff University Brain Research
  Imaging Centre (CUBRIC), School of Psychology
  Cardiff University
  Cardiff
  CF24 4HQ
  UK

  Email: WellsMT1@cardiff.ac.uk
  Tel: 02920 879628
  Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
  Mason T Wells, MSc
  Myfyriwr PhD
  Yr Ysgol Optometreg a Gwyddorau?r Golwg
  & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
  Prifysgol Caerdydd
  Heol Maindy
  Caerdydd
  CF24 4HQ
  DU

  E-bost: WellsMT1@caerdydd.ac.uk
  Ff?n: 02920 879628

  On 25/03/2020, 17:29, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

      Hi Mason

      I can't tell from those images except that it looks reasonable
      cheers
      Bruce
      On Wed, 25
      Mar 2020, Mason Wells wrote:

      External Email - Use Caution

Hi again Bruce,

I have now installed the relevant libpng packages and have freeview open. The segmentation doesn?t look brilliant in some areas. What do you think?

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau?r Golwg
& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: WellsMT1@caerdydd.ac.uk
Ff?n: 02920 879628

On 25/03/2020, 16:28, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@cardiff.ac.uk> wrote:

          External Email - Use Caution

  Hi Bruce,

  I get the following error message when I try to load freeview

  Setting up environment for FreeSurfer/FS-FAST (and FSL)
  FREESURFER_HOME   /usr/local/freesurfer
  FSFAST_HOME       /usr/local/freesurfer/fsfast
  FSF_OUTPUT_FORMAT nii.gz
  SUBJECTS_DIR      /usr/local/freesurfer/subjects
  MNI_DIR           /usr/local/freesurfer/mni
  FSL_DIR           /usr/local/fsl
  masontwells@masontwells-VIG800S:~$ freeview
  freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory

  Mason T Wells, MSc
  PhD student
  School of Optometry and Vision Sciences
  & Cardiff University Brain Research
  Imaging Centre (CUBRIC), School of Psychology
  Cardiff University
  Cardiff
  CF24 4HQ
  UK

  Email: WellsMT1@cardiff.ac.uk
  Tel: 02920 879628
  Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
  Mason T Wells, MSc
  Myfyriwr PhD
  Yr Ysgol Optometreg a Gwyddorau?r Golwg
  & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
  Prifysgol Caerdydd
  Heol Maindy
  Caerdydd
  CF24 4HQ
  DU

  E-bost: WellsMT1@caerdydd.ac.uk
  Ff?n: 02920 879628

  On 25/03/2020, 16:19, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

      something like

      freeview -v $SUBJECTS_DIR/<subject name>/mri/norm.mgz \
        -f $SUBJECTS_DIR/<subject name>/surf/?h.white

      cheers
      Bruce

      On Wed, 25 Mar 2020, Mason Wells wrote:

      External Email - Use Caution

Hi Bruce,

Thanks for getting back to me. Sorry, but I am not sure I follow what you mean here.
Could you please explain how I would check this?

Thanks again for your help.
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau?r Golwg
& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: WellsMT1@caerdydd.ac.uk
Ff?n: 02920 879628

On 25/03/2020, 16:11, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

  Hi Mason

  can you confirm that things look ok within FreeSurfer if you look at the
  surface over the volume in freeview?

  cheers
  Bruce
  On Wed, 25 Mar 2020, Mason Wells wrote:

       External Email - Use Caution

Hello Freesurfer developers,

I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all
command which finished without errors. However, the white/grey matter
boundaries are significantly misaligned with the subjects T1 (images
attached). Below are the steps I have taken to reach this point in the
analysis:

1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
2. Ran Feat

?         Distortion correction of the EPI

?         Motion correction

?         No smoothing

?         Highpass filter

?         No registration to whole brain

?         Register to T1_biascorr_brain

?         Register to standard space

3. Ran recon-all on T1_biascorr
4. Convert T1/T1_brain/orig(001) from mgz to nii
5. Check registration (using the SurfaceProjection command from the SamSrf
   package) which leads to the attached images named S1 and S1.

Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Platform: Linux 5.3.0-40-generic x86_64

Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon
Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

As you can see, the registration is significantly misaligned.

Can anyone offer any advice on this/suggest a way to rectify it?

Thanks in advance,

Mason

Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

Email: WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau?r Golwg

& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

E-bost: WellsMT1@caerdydd.ac.uk

Ff?n: 02920 879628

_______________________________________________
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End of Freesurfer Digest, Vol 193, Issue 37
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